Indices of various copeopod groups have been developed: https://noaa-edab.github.io/zooplanktonindex/CopeModResults.html
Now the question is, are the zooplankton available to herring larvae? We will explore data available on herring larvae in the EcoMon (and previous zooplankton) data.
Herring larvae data were added to the input dataset in the updated script https://github.com/NOAA-EDAB/zooplanktonindex/blob/main/data/VASTzoopindex_processinputs.R and all stations were re-mapped to OISST data to fill missing temperature values if necessary.
Where are herring larvae in each of our seasons?
herringfood_stn <- readRDS(here::here("data/herringfood_stn_all_OISST.rds"))
# make SST column that uses surftemp unless missing or 0
herringfood_stn <- herringfood_stn %>%
dplyr::mutate(sstfill = ifelse((is.na(sfc_temp)|sfc_temp==0), oisst, sfc_temp))
herringlarvae_stn_fall <- herringfood_stn %>%
#ungroup() %>%
filter(season_ng == "FALL",
year > 1981) %>%
mutate(AreaSwept_km2 = 1, #Elizabeth's code
#declon = -declon already done before neamap merge
Vessel = 1,
Dayofyear = lubridate::yday(date) #as.numeric(as.factor(vessel))-1
) %>%
dplyr::select(Catch_g = cluhar_100m3, #use megabenwt for individuals input in example
Year = year,
Month = month,
Dayofyear,
Vessel,
AreaSwept_km2,
Lat = lat,
Lon = lon,
#btm_temp, #this leaves out many stations
#sfc_temp, #this leaves out many stations
#oisst,
sstfill
) %>%
na.omit() %>%
as.data.frame()
herringlarvae_stn_spring <- herringfood_stn %>%
#ungroup() %>%
filter(season_ng == "SPRING",
year > 1981) %>%
mutate(AreaSwept_km2 = 1, #Elizabeth's code
#declon = -declon already done before neamap merge
Vessel = 1,
Dayofyear = lubridate::yday(date) #as.numeric(as.factor(vessel))-1
) %>%
dplyr::select(Catch_g = cluhar_100m3, #use megabenwt for individuals input in example
Year = year,
Month = month,
Dayofyear,
Vessel,
AreaSwept_km2,
Lat = lat,
Lon = lon,
#btm_temp, #this leaves out many stations
#sfc_temp, #this leaves out many stations
#oisst,
sstfill
) %>%
na.omit() %>%
as.data.frame()
nonzerofall <- herringlarvae_stn_fall |>
dplyr::filter(Catch_g > 0) #,
#Year > 1981)
nonzerospring <- herringlarvae_stn_spring |>
dplyr::filter(Catch_g > 0) #,
# Year > 1981)
Fall <- ggplot(data = ecodata::coast) +
geom_sf() +
geom_point(data = FishStatsUtils::northwest_atlantic_grid, aes(x = Lon, y = Lat), colour = "coral4", size=0.05, alpha=0.1) +
geom_point(data = nonzerofall, aes(x = Lon, y = Lat), colour = "blue", size=0.5, alpha=1) +
coord_sf(xlim =c(-78.5, -65.5), ylim = c(33, 45)) + #zoomed to Hatteras and N
xlab("") +
ylab("") +
ggtitle("Fall herring larvae 1982-2022")+
theme(plot.margin = margin(0, 0, 0, 0, "cm"))
Spring <- ggplot(data = ecodata::coast) +
geom_sf() +
geom_point(data = FishStatsUtils::northwest_atlantic_grid, aes(x = Lon, y = Lat), colour = "coral4", size=0.05, alpha=0.1) +
geom_point(data = nonzerospring, aes(x = Lon, y = Lat), colour = "blue", size=0.5, alpha=1) +
coord_sf(xlim =c(-78.5, -65.5), ylim = c(33, 45)) + #zoomed to Hatteras and N
xlab("") +
ylab("") +
ggtitle("Spring herring larvae 1982-2022")+
theme(plot.margin = margin(0, 0, 0, 0, "cm"))
Spring + Fall
Day of year and months herring larvae found (present, not abundance)
herringlarvae_stn_all <- dplyr::bind_rows(herringlarvae_stn_spring, herringlarvae_stn_fall)
hist(herringlarvae_stn_all$Dayofyear, xlim=c(0,365), breaks=366)
hist(herringlarvae_stn_all$Month, xlim=c(0,12), breaks=13)
Amount of herring larvae found (sum station volume over all years, not an abundance)
sumlarvae <- herringlarvae_stn_all |>
dplyr::group_by(Month) |>
dplyr::summarise(totlarvae = sum(Catch_g, na.rm = TRUE))
ggplot2::ggplot(sumlarvae, ggplot2::aes(x=Month, y=totlarvae)) +
ggplot2::geom_bar(stat = "identity")
So fall larvae, could be used to weight fall small copepods.
What years? Also just summing stations, not an abundance estimate
sumlarvaeyr <- herringlarvae_stn_all |>
dplyr::group_by(Year) |>
dplyr::summarise(totlarvae = sum(Catch_g, na.rm = TRUE))
ggplot2::ggplot(sumlarvaeyr, ggplot2::aes(x=Year, y=totlarvae)) +
ggplot2::geom_bar(stat = "identity")
# from each output folder in pyindex,
outdir <- here::here("pyindex")
moddirs <- list.dirs(outdir)
moddirs <- moddirs[-1]
# keep folder name
modnames <- list.dirs(outdir, full.names = FALSE)
# function to apply extracting info
getmodinfo <- function(d.name){
# read settings
modpath <- stringr::str_split(d.name, "/", simplify = TRUE)
modname <- modpath[length(modpath)]
settings <- read.table(file.path(d.name, "settings.txt"), comment.char = "",
fill = TRUE, header = FALSE)
n_x <- as.numeric(as.character(settings[(which(settings[,1]=="$n_x")+1),2]))
grid_size_km <- as.numeric(as.character(settings[(which(settings[,1]=="$grid_size_km")+1),2]))
max_cells <- as.numeric(as.character(settings[(which(settings[,1]=="$max_cells")+1),2]))
use_anisotropy <- as.character(settings[(which(settings[,1]=="$use_anisotropy")+1),2])
fine_scale <- as.character(settings[(which(settings[,1]=="$fine_scale")+1),2])
bias.correct <- as.character(settings[(which(settings[,1]=="$bias.correct")+1),2])
#FieldConfig
if(settings[(which(settings[,1]=="$FieldConfig")+1),1]=="Component_1"){
omega1 <- as.character(settings[(which(settings[,1]=="$FieldConfig")+2),2])
omega2 <- as.character(settings[(which(settings[,1]=="$FieldConfig")+3),1])
epsilon1 <- as.character(settings[(which(settings[,1]=="$FieldConfig")+4),2])
epsilon2 <- as.character(settings[(which(settings[,1]=="$FieldConfig")+5),1])
beta1 <- as.character(settings[(which(settings[,1]=="$FieldConfig")+6),2])
beta2 <- as.character(settings[(which(settings[,1]=="$FieldConfig")+7),1])
}
if(settings[(which(settings[,1]=="$FieldConfig")+1),1]=="Omega1"){
omega1 <- as.character(settings[(which(settings[,1]=="$FieldConfig")+3),1])
omega2 <- as.character(settings[(which(settings[,1]=="$FieldConfig")+4),1])
epsilon1 <- as.character(settings[(which(settings[,1]=="$FieldConfig")+3),2])
epsilon2 <- as.character(settings[(which(settings[,1]=="$FieldConfig")+4),2])
beta1 <- "IID"
beta2 <- "IID"
}
#RhoConfig
rho_beta1 <- as.numeric(as.character(settings[(which(settings[,1]=="$RhoConfig")+3),1]))
rho_beta2 <- as.numeric(as.character(settings[(which(settings[,1]=="$RhoConfig")+3),2]))
rho_epsilon1 <- as.numeric(as.character(settings[(which(settings[,1]=="$RhoConfig")+4),1]))
rho_epsilon2 <- as.numeric(as.character(settings[(which(settings[,1]=="$RhoConfig")+4),2]))
# read parameter estimates, object is called parameter_Estimates
if(file.exists(file.path(d.name, "parameter_estimates.RData"))) {
load(file.path(d.name, "parameter_estimates.RData"))
AIC <- parameter_estimates$AIC[1]
converged <- parameter_estimates$Convergence_check[1]
fixedcoeff <- unname(parameter_estimates$number_of_coefficients[2])
randomcoeff <- unname(parameter_estimates$number_of_coefficients[3])
}else if(file.exists(file.path(d.name, "parameter_estimates.txt"))){
reptext <- readLines(file.path(d.name, "parameter_estimates.txt"))
AIC <- as.double(reptext[grep(reptext, pattern = "AIC")+1])
converged <- reptext[grep(reptext, pattern = "Convergence_check")+1]
fixedcoeff <- as.integer(stringr::str_split(reptext[grep(reptext, pattern = "number_of_coefficients")+2],
boundary("word"))[[1]][2])
randomcoeff <- as.integer(stringr::str_split(reptext[grep(reptext, pattern = "number_of_coefficients")+2],
boundary("word"))[[1]][3])
}else{
AIC <- NA_real_
converged <- NA_character_
fixedcoeff <- NA_integer_
randomcoeff <- NA_integer_
}
#index <- read.csv(file.path(d.name, "Index.csv"))
# return model attributes as a dataframe
out <- data.frame(modname = modname,
n_x = n_x,
grid_size_km = grid_size_km,
max_cells = max_cells,
use_anisotropy = use_anisotropy,
fine_scale = fine_scale,
bias.correct = bias.correct,
omega1 = omega1,
omega2 = omega2,
epsilon1 = epsilon1,
epsilon2 = epsilon2,
beta1 = beta1,
beta2 = beta2,
rho_epsilon1 = rho_epsilon1,
rho_epsilon2 = rho_epsilon2,
rho_beta1 = rho_beta1,
rho_beta2 = rho_beta2,
AIC = AIC,
converged = converged,
fixedcoeff = fixedcoeff,
randomcoeff = randomcoeff#,
#index = index
)
return(out)
}
modcompare <- purrr::map_dfr(moddirs, getmodinfo)
modselect <- modcompare |>
dplyr::mutate(season = dplyr::case_when(stringr::str_detect(modname, "_fall_") ~ "Fall",
stringr::str_detect(modname, "spring") ~ "Spring",
stringr::str_detect(modname, "_all_") ~ "Annual",
TRUE ~ as.character(NA))) |>
dplyr::mutate(converged2 = dplyr::case_when(stringr::str_detect(converged, "no evidence") ~ "likely",
stringr::str_detect(converged, "is likely not") ~ "unlikely",
TRUE ~ as.character(NA))) |>
dplyr::mutate(copegroup = stringr::str_extract(modname, "[^_]+")) |>
#dplyr::mutate(modname = str_extract(modname, '(?<=allagg_).*')) |>
dplyr::group_by(copegroup, season) |>
dplyr::mutate(deltaAIC = AIC-min(AIC)) |>
dplyr::select(copegroup, modname, season, deltaAIC, fixedcoeff,
randomcoeff, use_anisotropy,
omega1, omega2, epsilon1, epsilon2,
beta1, beta2, AIC, converged2) |>
dplyr::arrange(copegroup, season, AIC)
# DT::datatable(modselect, rownames = FALSE,
# options= list(pageLength = 25, scrollX = TRUE),
# caption = "Comparison of delta AIC values using Restricted Maxiumum Likelihood (REML) for alternative fixed and random effects model structures. See text for model descriptions.")
# flextable::flextable(modselect) %>%
# #dplyr::select(-c(use_anisotropy,
# #omega1, omega2, epsilon1, epsilon2,
# #beta1, beta2))
# #) %>%
# flextable::set_header_labels(modname = "Model name",
# season = "Season",
# #deltaAIC = "dAIC",
# fixedcoeff = "N fixed",
# randomcoeff = "N random",
# converged2 = "Convergence") |>
# #flextable::set_caption("Comparison of delta AIC (dAIC) values using Restricted Maxiumum Likelihood (REML) for alternative fixed and random effects model structures, with number of fixed (N fixed) and random (N random) coefficients. See text for model descriptions associated with each model name.") %>%
# flextable::fontsize(size = 9, part = "all") %>%
# flextable::colformat_double(digits = 2) |>
# flextable::set_table_properties(layout = "autofit", width = 1)
These are the same for all models
for(d.name in moddirs[str_detect(moddirs, "herring")]){
modpath <- unlist(str_split(d.name, pattern = "/"))
modname <- modpath[length(modpath)]
cat(modname, "\n")
cat(paste0(""))
cat("\n\n")
}
herringlarvae_fall_500_test
stratlook <- data.frame(Stratum = c("Stratum_1",
"Stratum_2",
"Stratum_3",
"Stratum_4",
"Stratum_5",
"Stratum_6",
"Stratum_7"),
Region = c("AllEPU",
"her_sp",
"her_fa",
"MAB",
"GB",
"GOM",
"SS"))
# function to apply extracting info
getmodindex <- function(d.name){
# read settings
modpath <- stringr::str_split(d.name, "/", simplify = TRUE)
modname <- modpath[length(modpath)]
if(file.exists(file.path(d.name,"Index.csv"))){
index <- read.csv(file.path(d.name, "Index.csv"))
}else{
stopifnot()
}
# return model indices as a dataframe
out <- data.frame(modname = modname,
index
)
return(out)
}
modcompareindex <- purrr::map_dfr(moddirs, purrr::possibly(getmodindex, otherwise = NULL))
splitoutput <- modcompareindex %>%
dplyr::mutate(Season = modname |> map(str_split, pattern = "_") |> map_chr(c(1,2))) %>%
dplyr::mutate(Data = modname |> map(str_split, pattern = "_") |> map_chr(c(1,1))) %>%
dplyr::mutate(Estimate = ifelse(Estimate == 0, NA, Estimate)) |>
dplyr::left_join(stratlook) #%>%
#dplyr::filter(Region %in% c(GOM", "GB", "MAB","SS", "AllEPU")) use all regions
zoomax <- max(splitoutput$Estimate, na.rm=T)
zootsmean <- splitoutput %>%
dplyr::group_by(modname, Region) %>%
dplyr::mutate(fmean = mean(Estimate, na.rm=T))
plot_zooindices <- function(splitoutput, plotdata, plotregions, plottitle){
filterEPUs <- plotregions #c("her_sp", "her_fa", "MAB", "GB", "GOM", "SS", "AllEPU")
seasons <- splitoutput |> dplyr::filter(Data==plotdata) |> dplyr::select(Season) |> dplyr::distinct()
ncols <- dim(seasons)[1]
currentMonth <- lubridate::month(Sys.Date())
currentYear <- lubridate::year(Sys.Date())
if (currentMonth > 4) {
endShade <- currentYear
} else {
endShade <- currentYear - 1
}
shadedRegion <- c(endShade-9,endShade)
shade.alpha <- 0.3
shade.fill <- "lightgrey"
lwd <- 1
pcex <- 2
trend.alpha <- 0.5
trend.size <- 2
hline.size <- 1
line.size <- 2
hline.alpha <- 0.35
hline.lty <- "dashed"
label.size <- 5
hjust.label <- 1.5
letter_size <- 4
errorbar.width <- 0.25
x.shade.min <- shadedRegion[1]
x.shade.max <- shadedRegion[2]
setup <- list(
shade.alpha = shade.alpha,
shade.fill =shade.fill,
lwd = lwd,
pcex = pcex,
trend.alpha = trend.alpha,
trend.size = trend.size,
line.size = line.size,
hline.size = hline.size,
hline.alpha = hline.alpha,
hline.lty = hline.lty,
errorbar.width = errorbar.width,
label.size = label.size,
hjust.label = hjust.label,
letter_size = letter_size,
x.shade.min = x.shade.min,
x.shade.max = x.shade.max
)
fix<- splitoutput |>
dplyr::filter(Data %in% plotdata, #c("calfin"),
Region %in% filterEPUs) |>
dplyr::group_by(Region, Season) |>
dplyr::summarise(max = max(Estimate, na.rm=T))
p <- splitoutput |>
dplyr::filter(Data %in% plotdata, #c("calfin"),
Region %in% filterEPUs) |>
dplyr::group_by(Region, Season) |>
dplyr::left_join(fix) |>
dplyr::mutate(#Value = Value/resca,
Mean = as.numeric(Estimate),
SE = Std..Error.for.Estimate,
Mean = Mean/max,
SE = SE/max,
Upper = Mean + SE,
Lower = Mean - SE) |>
ggplot2::ggplot(ggplot2::aes(x = Time, y = Mean, linetype = modname, group = modname))+
ggplot2::annotate("rect", fill = setup$shade.fill, alpha = setup$shade.alpha,
xmin = setup$x.shade.min , xmax = setup$x.shade.max,
ymin = -Inf, ymax = Inf) +
ggplot2::geom_ribbon(ggplot2::aes(ymin = Lower, ymax = Upper, fill = Season), alpha = 0.5)+
ggplot2::geom_point()+
ggplot2::geom_line()+
ggplot2::ggtitle(plottitle)+
ggplot2::ylab(expression("Relative abundance"))+
ggplot2::xlab(ggplot2::element_blank())+
ggplot2::facet_wrap(Region~Season, ncol = ncols,
labeller = label_wrap_gen(multi_line=FALSE))+
ecodata::geom_gls()+
ecodata::theme_ts()+
ecodata::theme_facet()+
ecodata::theme_title() +
ggplot2::theme(legend.position = "bottom")
return(p)
}
plot_zooindices(splitoutput = splitoutput,
plotdata = "herringlarvae",
plotregions = c("her_sp", "her_fa", "MAB", "GB", "GOM", "SS", "AllEPU"),
plottitle = "Herring larvae")
for(d.name in moddirs[str_detect(moddirs, "herring")]){
modpath <- unlist(str_split(d.name, pattern = "/"))
modname <- modpath[length(modpath)]
cat(modname, "\n")
if(file.exists(paste0(d.name, "/ln_density-predicted.png"))){
cat(paste0(""))
}
cat("\n\n")
}
herringlarvae_fall_500_test